Cannot move 3D cursor or click to select objects
Whilst in the settings menu, Blender froze. After unsuccessfully trying to click on on some stuff, the preferences window disappeared. It turns out this somehow changed some input preferences.

Go to File -> User Preferences -> Input. Blender will very clearly indicate which options have been changed by displaying a "Restore" button next to the parent category:


Restore any unwanted mouse configs, and you're done. If the mouse settings are wrong for new projects as well, click on 'Save User Settings' after restoring.